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(-) Description

Title :  CRYSTAL STRUCTURE OF CD5_DIII
 
Authors :  B. Rodamilans
Date :  09 Feb 07  (Deposition) - 13 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  X,Y
Biol. Unit 1:  X  (1x)
Biol. Unit 2:  Y  (1x)
Keywords :  Srcr Group B Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Rodamilans, I. G. Munoz, E. Bragado-Nilsson, M. R. Sarrias, O. Padilla, F. J. Blanco, F. Lozano, G. Montoya
Crystal Structure Of The Third Extracellular Domain Of Cd5 Reveals The Fold Of A Group B Scavenger Cysteine-Rich Receptor Domain.
J. Biol. Chem. V. 282 12669 2007
PubMed-ID: 17322294  |  Reference-DOI: 10.1074/JBC.M611699200

(-) Compounds

Molecule 1 - T-CELL SURFACE GLYCOPROTEIN CD5
    Cell: B-LYMPHOCYTE
    Chains: X, Y
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293EBNA
    Expression System Common: HUMAN
    Expression System Plasmid: PCEP-PU
    Expression System Strain: HEK 293-EBNA
    Expression System Taxid: 9606
    Expression System Tissue: KIDNEY CELLS
    Fragment: CD5_DIII
    Gene: CD5, LEU1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LYMPHOCYTE ANTIGEN T1/LEU- 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : XY
Biological Unit 1 (1x): X 
Biological Unit 2 (1x):  Y

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2OTT)

(-) Sites  (0, 0)

(no "Site" information available for 2OTT)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1X:20 -X:56
2X:36 -X:95
3X:51 -X:102
4X:77 -X:85
5Y:20 -Y:56
6Y:36 -Y:95
7Y:51 -Y:102
8Y:77 -Y:85

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala Y:30 -Gln Y:31

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OTT)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRCR_2PS50287 SRCR domain profile.CD5_HUMAN35-133
276-368
 
159-268		  2-
X:11-103
Y:11-103
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRCR_2PS50287 SRCR domain profile.CD5_HUMAN35-133
276-368
 
159-268		  1-
X:11-103
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRCR_2PS50287 SRCR domain profile.CD5_HUMAN35-133
276-368
 
159-268		  1-
-
Y:11-103
-

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003477851ENSE00001145405chr11:60869930-60870087158CD5_HUMAN1-19190--
1.2ENST000003477852ENSE00001145421chr11:60882528-6088256639CD5_HUMAN19-32140--
1.3ENST000003477853ENSE00001145399chr11:60885647-60885952306CD5_HUMAN32-1341030--
1.4ENST000003477854ENSE00001119061chr11:60886387-6088644963CD5_HUMAN134-155220--
1.5ENST000003477855ENSE00001119062chr11:60886706-60887047342CD5_HUMAN155-2691150--
1.6ENST000003477856ENSE00001145387chr11:60889083-60889376294CD5_HUMAN269-367992X:7-102 (gaps)
Y:7-102 (gaps)		96
96
1.7ENST000003477857ENSE00001145383chr11:60890379-60890504126CD5_HUMAN367-409432X:102-104
Y:102-104		3
3
1.8ENST000003477858ENSE00000721687chr11:60891356-6089140954CD5_HUMAN409-427190--
1.9ENST000003477859ENSE00001198934chr11:60892504-60892623120CD5_HUMAN427-467410--
1.10ENST0000034778510ENSE00001198984chr11:60893223-6089331391CD5_HUMAN467-495290--
1.11ENST0000034778511ENSE00001397719chr11:60893760-608953191560CD5_HUMAN-00--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain X from PDB  Type:PROTEIN  Length:94
 aligned with CD5_HUMAN | P06127 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:98
                                   281       291       301       311       321       331       341       351       361        
            CD5_HUMAN   272 PKVQSRLVGGSSICEGTVEVRQGAQWAALCDSSSARSSLRWEEVCREQQCGSVNSYRVLDAGDPTSRGLFCPHQKLSQCHELWERNSYCKKVFVTCQD 369
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....eeeeeee.....ee....----hhhhhhhhhhhh....eeeeeee........eee....hhhhh...eee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SRCR_2  PDB: X:11-103 UniProt: 276-368                                                       - PROSITE
           Transcript 1 (1) Exon 1.6  PDB: X:7-102 (gaps) UniProt: 269-367 [INCOMPLETE]                                     -- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------1.7 Transcript 1 (2)
                 2ott X   7 PAVESRLVGGSSICEGTVEVRQGAQWAALCDS----SSLRWEEVCREQQCGSVNSYRVLDAGDPTSRGLFCPHQKLSQCHELWERNSYCKKVFVTCQD 104
                                    16        26        36 |    | 46        56        66        76        86        96        
                                                          38   43                                                             


Chain Y from PDB  Type:PROTEIN  Length:92
 aligned with CD5_HUMAN | P06127 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:98
                                   281       291       301       311       321       331       341       351       361        
            CD5_HUMAN   272 PKVQSRLVGGSSICEGTVEVRQGAQWAALCDSSSARSSLRWEEVCREQQCGSVNSYRVLDAGDPTSRGLFCPHQKLSQCHELWERNSYCKKVFVTCQD 369
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------SRCR-2ottY01 Y:14-103                                                                     - Pfam domains (1)
           Pfam domains (2) -------SRCR-2ottY02 Y:14-103                                                                     - Pfam domains (2)
         Sec.struct. author ...eeeeee.....eeeeeee.....ee...------hhhhhhhhhhhh...eeeeeee........eee....hhhhh...eee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SRCR_2  PDB: Y:11-103 UniProt: 276-368                                                       - PROSITE
           Transcript 1 (1) Exon 1.6  PDB: Y:7-102 (gaps) UniProt: 269-367 [INCOMPLETE]                                     -- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------1.7 Transcript 1 (2)
                 2ott Y   7 PAVESRLVGGSSICEGTVEVRQGAQWAALCD------SLRWEEVCREQQCGSVNSYRVLDAGDPTSRGLFCPHQKLSQCHELWERNSYCKKVFVTCQD 104
                                    16        26        36|      |46        56        66        76        86        96        
                                                         37     44
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2OTT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OTT)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: SRCR] (5)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain X,Y   (CD5_HUMAN | P06127)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0005044    scavenger receptor activity    Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs).
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0008037    cell recognition    The process in which a cell in an organism interprets its surroundings.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CD5_HUMAN | P06127: 2ja4 2jop 2jp0

(-) Related Entries Specified in the PDB File

2ja4